Working with Workflows in PEITHO: Import, Export, and Execution • PEITHO

Introduction

This vignette demonstrates how to use the PEITHO package to manage, export, import, and execute workflows. The workflow system in PEITHO allows you to define a sequence of steps (such as data fetching, processing, or analysis), save and share workflows as zip files, and re-import or modify them for further use. This guide is aimed at users with basic R knowledge, but no advanced R expertise is required.

Prerequisites

Install the PEITHO package from GitHub if not already installed:

devtools::install_github("Pandora-IsoMemo/PEITHO")
Load the package:

library(PEITHO)

For development only, you may use devtools::load_all() instead of library(PEITHO).

Loading the Example Workflow

You can create a workflow object from your own files by specifying a path, or use the example workflow included with PEITHO by passing an empty string as the path:

my_wf <- new_workflow(workflow_file_paths = workflow_file_paths(path = ""))

## INFO [2026-02-12 08:01:26] Creating empty results.json file.

## INFO [2026-02-12 08:01:26] Parsing command simple_split for step 1

## INFO [2026-02-12 08:01:26] Parsing command fetch_WebText for step 2

## INFO [2026-02-12 08:01:26] Parsing command unlist for step 3

## INFO [2026-02-12 08:01:26] Parsing command paste for step 4

## INFO [2026-02-12 08:01:26] Parsing command paste for step 5

## INFO [2026-02-12 08:01:26] Parsing command gsub for step 6

## INFO [2026-02-12 08:01:26] Parsing command simple_split for step 7

## INFO [2026-02-12 08:01:26] Parsing command simple_split for step 8

## INFO [2026-02-12 08:01:26] Parsing command fetch_WebText for step 9

## INFO [2026-02-12 08:01:26] Parsing command unlist for step 10

## INFO [2026-02-12 08:01:26] Parsing command paste for step 11

## INFO [2026-02-12 08:01:26] Parsing command paste for step 12

## INFO [2026-02-12 08:01:26] Parsing command paste for step 13

Exporting a Workflow as a Zip File

You can export the current workflow setup (all relevant files) as a zip archive (here with the .peitho extension):

zipfile_path <- "./examples/my_workflow.peitho"
save_as_zip(my_wf, file = zipfile_path)

## INFO [2026-02-12 08:01:26] Creating directory './examples' for saving zip file.

Running a Workflow

To execute the workflow, use the run() function. You can specify which steps to run (e.g., from step 1 to 5):

my_run_1 <- run(my_wf, from = 1, to = 5)

## INFO [2026-02-12 08:01:26] Running step 1 of 5

## INFO [2026-02-12 08:01:26]   Operation 'simple_split': 3 results

## INFO [2026-02-12 08:01:26] Running step 2 of 5

## INFO [2026-02-12 08:01:29]   3 loop iterations for operation 'fetch_WebText':

## WARN [2026-02-12 08:01:29]      WARNING! Multiple results per iteration! Ensure that downstream steps handle list inputs.

## INFO [2026-02-12 08:01:29] Running step 3 of 5

## INFO [2026-02-12 08:01:29]   3 loop iterations for operation 'unlist':

## WARN [2026-02-12 08:01:29]      WARNING! Multiple results per iteration! Ensure that downstream steps handle list inputs.

## INFO [2026-02-12 08:01:29] Running step 4 of 5

## INFO [2026-02-12 08:01:29]   3 loop iterations for operation 'paste':

## INFO [2026-02-12 08:01:29]      3 single results.

## INFO [2026-02-12 08:01:29] Running step 5 of 5

## WARN [2026-02-12 08:01:29] WARNING! Detected list argument(s) for operation 'paste', but 'loop' is set to 'no'.

## INFO [2026-02-12 08:01:29]   Operation 'paste': single result

After running, you can inspect the results:

length(my_run_1$state$last_result)

## [1] 1

PEITHO:::trunc(my_run_1$state$last_result, n_char = 100)

## [1] "Main page---Contents---Current events---Random article---About Wikipedia---Contact us---Help---Learn ..."

Importing and Modifying a Workflow from a Zip File

To import a workflow from a zip file, first define the directory where the workflow files will be extracted. You may also modify the workflow steps (for example, by editing commands.json or inputs.json in the extracted folder) before running it.

zipfile_path <- "./examples/my_workflow.peitho"

my_wf_imported <- PEITHO::import_workflow(
  zipfile = zipfile_path,
  extract_dir = "./examples/peitho_import"
)

## INFO [2026-02-12 08:01:30] Parsing command simple_split for step 1

## INFO [2026-02-12 08:01:30] Parsing command fetch_WebText for step 2

## INFO [2026-02-12 08:01:30] Parsing command unlist for step 3

## INFO [2026-02-12 08:01:30] Parsing command paste for step 4

## INFO [2026-02-12 08:01:30] Parsing command paste for step 5

## INFO [2026-02-12 08:01:30] Parsing command gsub for step 6

## INFO [2026-02-12 08:01:30] Parsing command simple_split for step 7

## INFO [2026-02-12 08:01:30] Parsing command simple_split for step 8

## INFO [2026-02-12 08:01:30] Parsing command fetch_WebText for step 9

## INFO [2026-02-12 08:01:30] Parsing command unlist for step 10

## INFO [2026-02-12 08:01:30] Parsing command paste for step 11

## INFO [2026-02-12 08:01:30] Parsing command paste for step 12

## INFO [2026-02-12 08:01:30] Parsing command paste for step 13

You can now run the imported (and possibly modified) workflow and inspect the results as before:

my_run_2 <- run(my_wf_imported, from = 1, to = 4)

## INFO [2026-02-12 08:01:30] Running step 1 of 4

## INFO [2026-02-12 08:01:30]   Operation 'simple_split': 3 results

## INFO [2026-02-12 08:01:30] Running step 2 of 4

## INFO [2026-02-12 08:01:32]   3 loop iterations for operation 'fetch_WebText':

## WARN [2026-02-12 08:01:32]      WARNING! Multiple results per iteration! Ensure that downstream steps handle list inputs.

## INFO [2026-02-12 08:01:32] Running step 3 of 4

## INFO [2026-02-12 08:01:32]   3 loop iterations for operation 'unlist':

## WARN [2026-02-12 08:01:32]      WARNING! Multiple results per iteration! Ensure that downstream steps handle list inputs.

## INFO [2026-02-12 08:01:32] Running step 4 of 4

## INFO [2026-02-12 08:01:32]   3 loop iterations for operation 'paste':

## INFO [2026-02-12 08:01:32]      3 single results.

length(my_run_2$state$last_result)

## [1] 3

PEITHO:::trunc(my_run_2$state$last_result, n_char = 100)

## [1] "Main page---Contents---Current events---Random article---About Wikipedia---Contact us---Help---Learn ..., \\nMain page---Contents---Current events---Random article---About Wikipedia---Contact us---Help---Learn ..., \\nMain page---Contents---Current events---Random article---About Wikipedia---Contact us---Help---Learn ..."

Summary

PEITHO’s workflow system allows you to:

Load and execute multi-step workflows from configuration files
Export workflows as zip files for sharing or backup
Import and modify workflows from zip files
Inspect and print results from workflow execution

This makes it easy to share, reuse, and adapt complex analysis pipelines in a reproducible way.